Severe acute respiratory syndrome coronavirus (SARS-CoV) infection often caused severe end stage lung disease and organizing phase diffuse alveolar damage, especially in the elderly. The virus-host interactions that governed development of these acute end stage lung diseases and death are unknown. To address this question, in collaboration with scientists at the University of North Carolina, we evaluated the role of innate immune signaling in protection from human (Urbani) and mouse adapted SARS-CoV, designated MA15. In contrast to most models of viral pathogenesis, infection of type I, type II or type III interferon knockout mice on a 129 background, with either Urbani or MA15 viruses resulted in clinical disease outcomes, including transient weight loss, denuding bronchiolitis and alveolar inflammation and recovery, identical to that seen in infection of wildtype mice. This suggests that type I, II and III interferons play minor roles in regulating SARS pathogenesis in mouse models. In contrast, infection of STAT1-/- mice resulted in severe disease, high virus titer, extensive pulmonary lesions and mortality by day 9 and 30 post-infection with MA15 or Urbani viruses, respectively. Urbani SARS-CoV infection in STAT1-/- mice caused disseminated infection involving the liver, spleen and others tissues after day 9. These findings demonstrated that SARS-CoV pathogenesis is regulated by a STAT1 dependent but type I, II and III interferon independent mechanism. In contrast to a well-documented role in innate immunity, we propose that STAT1 primarily protects mice via its role as an antagonist of unrestrained cell proliferation. The genome of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) contains eight open reading frames (ORFs) that encode novel proteins. These accessory proteins are dispensable for in vitro and in vivo replication and thus may be important for other aspects of virus-host interactions. In collaboration with scientists from the Laboratory of Immunology in NIAID, we investigated the functions of the largest of the accessory proteins, the ORF 3a protein, using a 3a-deficient strain of SARS-CoV. Cell death of Vero cells after infection with SARS-CoV was reduced upon deletion of ORF 3a. Electron microscopy of infected cells revealed a role for ORF 3a in SARS-CoV induced vesicle formation, a prominent feature of cells from SARS patients. In addition, we found that ORF 3a is both necessary and sufficient for SARS-CoV-induced Golgi fragmentation and that the 3a protein accumulates and localizes to vesicles containing markers for late endosomes. Finally, overexpression of ADP-ribosylation factor 1 (Arf1), a small GTPase essential for the maintenance of the Golgi apparatus, restored Golgi morphology during infection. These results establish an important role for ORF 3a in SARS-CoV-induced cell death, Golgi fragmentation, and the accumulation of intracellular vesicles. The goal of our SARS program was driven by the public health need in 2003 for animal models for the evaluation of vaccines and immunoprophylaxis strategies. We developed mouse, hamster and non-human primate models and collaborated with several scientists from academic institutions and pharmaceutical companies to evaluate the efficacy of candidate vaccines. We have also investigated the pathogenesis of disease in the murine models of SARS. However, since SARS has not reappeared in epidemic form and pandemic influenza is a more imminent threat, we have discontinued active research in SARS and have re-directed the resources to work on pandemic influenza vaccines.